#include <iostream>
#include <vector>
#include <string>

#include "blosum.h"

using namespace std;

void fillTestSequences(vector<string> & container);

int main ( int argc, char **argv ) {
    Blosum blosum;

if (argc==1) {
	blosum.setAlphabet("abc");
   vector<string> sequences;
   fillTestSequences(sequences);
   blosum.setSequences(sequences);
}

if (argc==2) {
    blosum.fillSequencesFromFile( argv[1] );
}

if (argc>2) {
        cout<<"Błędna ilość parametrów"<<endl;
        return 1;
}
 
  blosum.calculate();
  blosum.getBlosumMatrix();
  blosum.saveBlosumMatrix("alleluja.txt");

return 0;
}


void fillTestSequences(vector<string> & container) {
    container.reserve(7);
    container.push_back("CCAAABAC");
    container.push_back("CCAABBAB");
    container.push_back("BBCACBAB");
    container.push_back("CBCACBAB");
    container.push_back("CCCABBAB");
    container.push_back("CCCBBBAB");
}
